Ethanol Production
Enzymes
Industrial Biotechnology
Nutrition & Human Health
Plant Cell Wall Biology
Plant Physiology
Ethanol Production
Wyman CE, Dale BE, Elander Rt, Holtzapple M, Ladisch MR, Lee YY. 2005. Comparative sugar recovery data from laboratory scale application of leading pretreatment technologies to corn stover. Bioresour technol. 96(18):2026-32.
Mosier N, Hendrickson R, Ho N, Sedlak M, Ladisch MR. 2005. Optimization of pH controlled liquid hot water pretreatment of corn stover. Bioresour technol. 96(18):1986-93.
Wyman CE, Dale BE, Elander Rt, Holtzapple M, Ladisch MR, Lee YY. 2005. Coordinated development of leading biomass pretreatment technologies. Bioresour technol. 96(18):1959-66.
Mosier NS, Hendrickson R, Brewer M, Ho N, Sedlak M, Dreshel R, Welch G, Dien BS, Aden A, Ladisch MR. 2005. Industrial scale-up of pH-controlled liquid hot water pretreatment of corn fiber for fuel ethanol production. Appl Biochem Biotechnol. 125(2):77-97.
Mosier N, Wyman C, Dale B, Elander R, Lee YY, Holtzapple M, Ladisch M. 2005. Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresour technol. 96(6):673-86.
Mosier NS, Wilker JJ, Ladisch MR. 2004. Rapid chromatography for evaluating adsorption characteristics of cellulase binding domain mimetics. Biotechnol Bioeng. 86(7):756-64.
Mosier NS, Ladisch CM, Ladisch MR. 2002. Characterization of acid catalytic domains for cellulose hydrolysis and glucose degradation. Biotechnol Bioeng. 79(6):610-8.
Mosier NS, Hall P, Ladisch CM, Ladisch MR. 1999. Reaction kinetics, molecular action, and mechanisms of cellulolytic proteins. Adv Biochem Eng Biotechnol. 65:23-40.
Sarikaya A, Ladisch MR. 1997. Mechanism and potential applications of bio-ligninolytic systems in a CELSS. Appl Biochem Biotechnol. 62(2-3):131-49.
Kohlmann KL, Westgate P, Velayudhan A, Weil J, Sarikaya A, Brewer MA, Hendrickson RL, Ladisch MR. 1996. Enzyme conversion of lignocellulosic plant materials for resource recovery in a Controlled Ecological Life Support System. Adv Space Res. 18(1-2):251-65.
Weil J, Westgate P, Kohlmann K, Ladisch MR. 1994. Cellulose pretreatments of lignocellulosic substrates. Enzyme Microb technol. Nov;16(11):1002-4.
Goldberg, RA. Gruppo Ferruzzi: Economics, Politics and Ethanol. Harvard Business School Case 588-002.
Ladisch MR, Hong J, Voloch M, Tsao Gt. 1981. Cellulase kinetics. Basic Life Sci. 18:55-83.
Gong CS, Ladisch MR, Tsao Gt. 1977. Cellobiase from trichoderma viride: purification, properties, kinetics, and mechanism. Biotechnol Bioeng. Jul;19(7):959-81.
Ladisch, M.R., Dyck, K. 1979. Dehydration of ethanol: new approach gives positive energy balance. Science, 205:898-900.
Ladisch MR, Voloch M, Hong J, Blenkowski P, Tsao Gt. 1984. Cornmeal Adsorber for Dehydrating Ethanol Vapors. Ind. Eng. Chem. Process Des. Dev. 23: 437-443.
Enzymes
Ekborg NA, Morrill W, Burgoyne AM, Li L, Distel DL, 2007. CelAB, a Multifunctional Cellulase Encoded by Teredinibacter turnerae T7902T, a Culturable Symbiont Isolated from the Wood-boring Marine Bivalve, Lyrodus pedicellatus. Appl Environ Microbiol. 73(23):7785-8.
Taylor LE, Henrissat B, Coutinho PM, Ekborg NA, Hutcheson SW, Weiner RM. 2006. Complete Cellulase System in the Marine Bacterium Saccharophagus degradans Strain 2-40T. J. Bacteriol. 188: 3849-3861.
Ekborg NA, Taylor LE, Longmire AG, Henrisatt B, Weiner RM, Hutcheson SW. 2006. Genomic and Proteomic Analysis of the Agarolytic System Expressed by Saccharophagus degradans 2-40. Appl. Environ. Microbiol. 72: 3396-3405.
Henshaw J, Horne A, van Bueren AL, Money V, Bolam DN, Czjzek M, Ekborg NA, Weiner R, Hutcheson SW, Davies GJ, Boraston AB, Gilbert HJ. 2006. Family 6 Carbohydrate Binding Modules in beta-Agarases Display Exquisite Selectivity for the Non-Reducing Termini of Agarose Chains. J Biol Chem. 281(25), 17099-17107.
Ekborg NA, Gonzales JM, Howard MB, Taylor LE , Hutcheson SW, Weiner, RM. 2005. Saccharophagus degradans gen. nov., sp. nov., A Versatile Marine Bacterial Degrader of Complex Polysaccharides. Int J Syst Evol Microbiol. Jul;55(4):1545-9.
Howard MB, Ekborg NA, Taylor LE, Hutcheson SW, Weiner RM. 2004. Identification and Analysis of Polyserine Linker Domains in Prokaryotic Proteins with Emphasis on the Marine Bacterium “Microbulbifer degradans”. Protein Sci. 13(5):1422-5.
Howard MB, Ekborg NA, Taylor LE 2nd, Weiner RM, Hutcheson SW. 2004. Chitinase B of "Microbulbifer degradans" 2-40 Contains Two Catalytic Domains with Different Chitinolytic Activities. J Bacteriol. 186(5):1297-303.
Howard MB, Ekborg NA, Weiner RM, Hutcheson SW. 2003. Detection and Characterization of Chitinases and other Chitin-modifying Enzymes. J Ind Microbiol Biotechnol. 30(11):627-35.
Weiner RM, Taylor LE, Ekborg NA, and Whitehead LA. 2000. Degradosomes: Potential Importance in the Ocean’s Carbon Cycle and in Aquaculture and Algalculture. Recent Advances in Marine Science and Technology, 259-268.
Industrial Biotechnology
Yang JC, Durkin AS, Madupu R, Ekborg NA, Henrissat B, Schwartz S, Mougous JC, Pedamallu CS, Fields L, Trindade-Silva AE, Soares CA, Elshahawi S, Hanora A, Haygood MG, Posfai J, Benner J, Swaim C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Zehr J, Teplitski M, Ward N, Eisen JA, Badger JH, and Distel DL. 2009. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (family Teredinidae). PLoS One. 4(7):e6085.
Weiner RM, Taylor II LE, Henrissat B, Hauser L, Land M, Coutinho PM, RancurelC, Saunders EH, Longmire AG, Ekborg NA, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, LamedR, Richardson PM, Borovok I, Hutcheson S. 2008. Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans strain 2-40T. PLoS Genet. 4(5):e1000087.
Raab RM, Tyo K, Stephanopoulos G. 2005. Metabolic Engineering, Advances in Biochemical Engineering/ Biotechnology, Springer-Verlag GmbH; Volume 100:1-16
Raab RM, Stephanopoulos G. 2004. "Dynamics of Gene Silencing by RNA Interference," Biotechnology & Bioengineering, 88(1):121-132.
Schmitt WA, Raab RM, Stephanopoulos G. 2004. "Elucidation of Gene Interaction Networks through time-lagged Correlation Analysis of transcriptional Data," Genome Research, 14(8):1654-1663
Jensen K, Rigoutsos I, Stephanopoulos G. 2003. "Syntactic Pattern Discovery as a Generic tool in Systems Biology," Proceedings of the American Chemical Society Annual Meeting.
de la Vega H, Specht CA, Liu Y, Robbins PW. 1998. Chitinases are a multi-gene family in Aedes, Anopheles and Drosophila. Insect Molecular Biology 7: 233-239
Mishra C, Semino CE, McCreath KJ, de la Vega H, Jones BJ, Specht CA, Robbins PW. 1997. Cloning and expression of two chitin deacetylase genes of Saccharomyces cerevisiae. Yeast 13: 327-336
de la Vega H, Specht CA, Semino CE, Robbins PW, Eichenger D, Caplivsky D, Ghosh S, Samuelson J. 1997. Cloning and expression of chitinases of Entamoeba. Molecular and Biochemical Parasitology 85: 139-147
Rosenthal B, Mai Z, Caplivski D, Ghosh S, de la Vega H, Graf T, Samuelson J. 1997. Evidence for the bacterial origin of genes encoding fermentation enzymes of the amitochondriate protozoan parasite Entamoeba histolytica. Journal of Bacteriology 179: 3736-3745.
de la Vega H, Specht CA, Chau A, Semino CE, Robbins PW, Eichinger D, Caplivski D, Ghosh S, Samuelson J. 1997. Cyst-specific exochitinases of Entamoeba contain unique hydrophilic repeats at their amino termini. Arch of Med Res 28: suppl. S143-s146
Bedbrook J, Ausubel FM. 1976. Recombination between bacterial plasmids leading to the formation of plasmid multimers. Cell 9:707-716.
Ruvkun GB, Ausubel FM. 1981. A general method for site directed mutagenesis in prokaryotes: Construction of mutations in symbiotic nitrogen fixation genes of Rhizobium meliloti. Nature 289:85-88.
Ausubel FM, and Ruvkun GB. 1981. A general method for site-directed mutagenesis in Gram negative prokaryotes: Isolation of nitrogen fixation mutants in Rhizobium meliloti. In: Microbiology 1981 (D. Schlessinger, ed.) American Society for Microbiology, Washington, D.C., pp. 124-127.
Nutrition & Human Health
Raab RM. 2006. Integrating Genome Scale tools for Studying Energy Homeostasis. Nutrition & Metabolism, 3:40.
Raab RM, Bullen J, Kelleher J, Mantzoros C, Stephanopoulos G. 2005. Regulation of Mouse Hepatic Genes in Response to Diet Induced Obesity, Insulin Resistance and Fasting. Nutrition & Metabolism, 2:15.
Wong M, Raab RM, Rigoutsos I, Kelleher J, Stephanopoulos G. 2004. Metabolic and transcriptional Patterns Accompanying Glutamine Depletion and Repletion in Mouse Hepatoma Cells: A Model for Physiological Regulatory Networks. Physiological Genomics, 16(2):247-255.
Wang F, Raab RM, Washabaugh MW, Buckland BC. 2000. Gene therapy and Metabolic Engineering. Metabolic Engineering, 2:126-139.
Olsson ML, Hill C, de la Vega H, Liu P, Stroud MR, Valdinocci J, Moon S, Clausen H, Kruskall MS. 2004. Universal Red Blood Cells - Enzymatic Conversion of Blood Group A and B Antigens. Transfusion Clinique et Biologique 11, 33 - 39.
Jensen K, Jung G, Rigoutsos I, Stephanopoulos G. 2003. In Silico Discovery and Design of Antimicrobial Peptides. Proceedings of the American Institute of Chemical Engineers Annual Meeting.
Plant Cell Wall Biology
Keegstra K, Walton J. 2006. Plant science. Beta-glucans—brewer's bane, dietician's delight. Science. 311(5769):1872-3.
Liepman AH, Wilkerson CG, Keegstra K. 2005. Expression of cellulose synthase-like (Csl) genes in insect cells reveals that CslA family members encode mannan synthases. Proc Natl Acad Sci USA. 102(6):2221-6
Girke t, Lauricha J, tran H, Keegstra K, Raikhel N. 2004. the Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol. 136(2):3003-8
Keegstra K, Raikhel N (2001) Plant glycosyltransferases. Curr Opin Plant Biol 4: 219-224
Perrin RM, DeRocher AE, Bar-Peled M, Zeng W, Norambuena L, Orellana A, Raikhel NV, Keegstra K (1999) Xyloglucan fucosyltransferase, an enzyme involved in plant cell wall biosynthesis. Science 284: 1976-1979
Perrin R, Wilkerson C, Keegstra K (2001) Golgi enzymes that synthesize plant cell wall polysaccharides: Finding and evaluating candidates in the genomic era. Plant Mol Biol 47: 115-130
Faik A, Price NJ, Raikhel NV, Keegstra K (2002) An Arabidopsis gene encoding an α-xylosyltransferase involved in xyloglucan biosynthesis. Proc Natl Acad Sci USA 99: 7797-7802
Keegstra K, talmadge KW, Bauer WD, Albersheim P. 1973. the Structure of Plant Cell Walls: III. A Model of the Walls of Suspension-cultured Sycamore Cells Based on the Interconnections of the Macromolecular Components. Plant Physiol. Jan;51(1):188-197.
Bauer WD, talmadge KW, Keegstra K, Albersheim P. 1973. the Structure of Plant Cell Walls: II. the Hemicellulose of the Walls of Suspension-cultured Sycamore Cells. Plant Physiol. Jan;51(1):174-187.
talmadge KW, Keegstra K, Bauer WD, Albersheim P. 1973. the Structure of Plant Cell Walls: I. the Macromolecular Components of the Walls of Suspension-cultured Sycamore Cells with a Detailed Analysis of the Pectic Polysaccharides. Plant Physiol. Jan;51(1):158-173.
English PD, Maglothin A, Keegstra K, Albersheim P. 1972. A Cell Wall-degrading Endopolygalacturonase Secreted by Colletotrichum lindemuthianum. Plant Physiol. Mar;49(3):293-298.
Keegstra K, Albersheim P. 1970. the Involvement of Glycosidases in the Cell Wall Metabolism of Suspension-cultured Acer pseudoplatanus Cells. Plant Physiol. Jun;45(6):675-678.
Plant Physiology
Quinto C, de la Vega H, Flores M, Fernandez L, Soberan G, Palacios R. 1982. Reiteration of Nitrogen Fixation Gene sequences in Rhizobium phaseoli. Nature 299:724-726
Palacios R, Quinto C, Leemans J, Flores M, de la Vega H, Martanez E. 1985. Reiterated Nitrogenase Reductase genes in Rhizobium phaseoli. Molecular Form and Function of the Plant Genome. (Eds.Louis van Vloten-Doting, Gert S.P. Groot, and Timothy C. Hall). Plenum Publishing Corporation
Quinto C, De la Vega H, Flores M, Leemans J, Cevallos MA, Pardo MA, Azpiroz R, Girard ML, Calva E, Palacios R. 1985. Nitrogenase Reductase: A functional multigene family in Rhizobium phaseoli. Proc Nat Acad Sci USA : 82 :1170 - 1174
Palacios R, Quinto C, de la Vega H, Flores M, Fernandez L, Hernandez M, Ballado T, Soberan-Chavez, J. 1983. General Organization of Nitrogen Fixation Genes in Rhizobium phaseoli Molecular Genetics of the Bacteria Plant Interaction (ed. A. Pahler) Springer-Verlag Berlin Heidelberg
Mitchell AZ, Hanson MR, Skvirsky RC, Ausubel RM. 1980. Anther culture of Petunia: Genotypes with high frequency of callus, root, or plantlet formation. Z. Pflanzenphysiol. 100:131-146.
Ausubel, FM (2000) Arabidopsis Genome: A Milestone in Plant Biology. Plant Physiol. 124:1451-1454.